Synthesis of 1-(2-Deoxy-β-D-ribofuranosyl)benzimidazole via Cyclonucleosides

Abstract

Starting from 2-chlorobenzimidazole and 1-O-acetyl-2,3,5-tri-O-benzoylribofuranose a β-D-ribonucleoside of 2-chlorobenzimidazole was obtained using Vorbrüggen's procedure. This compound was derivatized to a 2,2′-S-cyclonucleoside via 2′-O-tosylation and thiourea treatment. The cyclonucleoside was converted to 1-(2-deoxy-β-D-ribo-furanosyl) benzimidazole by Raney nickel desulfurization.     

Synthesis of 9-(2-Deoxy-β-D-ribofuranosyl)purine-2-thione

Abstract

A synthesis of 9-(2-deoxy-β-D-ribofuranosyl)purine-2-thione was performed by desulfurization of 2′-deoxy-6-thioguanine to give 2-amino-9-(2-deoxy-β-D-ribofuranosyl)purine, diazotization with chloride replacement to give 2-chloro-9-(2-deoxy-β-D-ribofuranosyl)purine, and the replacement of chloride with sulfur using thiolacetic acid and deacetylation.     

Reaction of 2-Deoxy-2-C-(3-bromoacetoxypropyl)-α-D-arabinofuranosides with Oligonucleotide1

Abstract

Reaction of methyl 2-deoxy-2-C-(3-bromoacetoxypropyl)-α-D-arabinofuranosides, prepared from methyl 2,3-anhydro-α-D-ribofuranoside, with oligodeoxyribonucleotide (21mer) in acetonitrile-H₂O (pH 7) and subsequent treatment with piperidine resulted in the cleavage of the nucleotide chain at the position G, A, and C.     

Derivatives of 1-(2-Deoxy-2-fluoro-β-D-arabinofuranosyl)-5-phenyluracil and 5-Benzyluracil. Synthesis and Biological Properties

Abstract

A number of 1-(2-deoxy-2-fluoro-β-D-arabinofuranosyl)uracil and -cytosine nucleosides substituted at the 5 position with a nitrophenyl or nitrobenzyl group were synthesized from 5-phenyl- and 5-benzyluracil via condensation of the fluorinated sugar, followed by nitration. The corresponding amino analogues were also prepared by reduction of the nitro nucleosides. The uracil nucleosides were converted into the corresponding cytosine nucleosides by way of the triazole intermediates. None of these nucleosides exhibited significant activity against herpes simplex virus type 1 in Vero cells. However, cytosine nucleosides containing the o-nitrophenyl, p-nitrophenyl, p-nitrobenzyl or p-aminobenzyl substituent were found to be toxic (even at 1 μM) to uninfected Vero cells, although they were essentially nontoxic in HL-60 cells. The 5′-monophosphates of the uracil nucleosides were inhibitors of the reaction catalyzed by purified Ehrlich ascites carcinoma thymidylate synthase, the 5-phenyluracil nucleotides causing a strong inhibition, competitive vs dUMP, described by the K_i value of 0.01 μM.     

Nucleosides. 131. The Synthesis of 5-(2-Chloro-2-Deoxy-β-D-arabino-Furanosyl)Uracil. Reinterpretation of Reaction of ψ-Uridine With α-Acetoxyisobutyryl Chloride. Studies Directed Toward the Synthesis of 2′-Deoxy-2′-Substituted Arabino-Nucleosides. 2

Abstract

Treatment of ψ-uridine (3) with α-acetoxyisobutyryl chloride in acetonitrile gave, after deprotection, a mixture of four products: 5-(2-chloro-2-deoxy-β-D-arabinofuranosyl)uracil (10a), its 3′-chloro xylo isomer (11a), 2′-chloro-2′-deoxy-ψ-uridine (9a) and 4,2′-anhydro-ψ-uridine (8a). Each component was isolated by column chromatography. Compound 9 was converted to the known 1,3-dimethyl derivative 2 by treatment with DMF-dimethylacetal. Treatment of 10 and 11 with NaOMe/MeOH afforded the same 4,2′-anhydro-C-nucleoside 8. The 1,3-dimethyl analogues of 10 and 11, however, were converted to 2′,3′-anhydro-1,3-dimethyl-ψ-uridine (13) upon base treatment. The epoxide 13 was also prepared in good yield by treatment of 10 and 11 with DMF-dimethylacetal.     

Synthesis and Physicochemical Properties of 2′-Deoxy- 2′,2″-difluoro-β-D-ribofuranosyl and 2′-Deoxy-2′,2″- difluoro-α-D-ribofuranosyl Oligonucleotides

Abstract

We present procedures for nucleoside and oligonucleotide synthesis, binding affinity (T _m) and structural analysis (CD spectra) of 2′-deoxy-2′,2″-difluoro-α-D-ribofuranosyl and 2′-deoxy-2′,2″-difluoro-β-D-ribofuranosyl oligothymidylates. Possible reasons for the thermal instability of duplexes formed between these compounds and RNA or DNA targets are discussed.     

Inhibition of 5-α-Reductase (TYPE-II) Expression by Antisense 3′-Deoxy-(2′-5′) Oligonucleotide Chimeras

Abstract

ABSTRACT: 3′-Deoxy-(2′-5′) oligonucleotides bind selectively to complementary RNA but not to DNA. 3′-Deoxy-(2′-5′) phosphorothioate ODN chimeras embedded with a short stretch of 3′-5′ phosphorothioate cassette are potent inhibitors of steroid 5-α-reductasc expression with significantly less non-specific interactions in cell culture.     

Nucleosides. II. Synthesis and Properties of 3,4-Diaryl-4,5-dihydro-1-(β-D-ribofuranosyl)-1,2,4-triazole-5-thiones

Abstract

3,4-Diaryl-4,5-dihydro-1,2,4-triazole-5-thiones (1a-c) were silylated to give compounds (2a-c) which were condensed with 1-O-acetyl-2,3,5-tri-O-benzoyl-β-D-ribofuranose (3) in the presence of trimethylsilyl trifluoromethane sulfonate to afford the corresponding nucleosides 4a-c. Treatment of 4a-c with sodium methoxide in methanol at room temperature afforded the debenzoylated nucleosides 5a-c. The reaction of 5a with acetone in the presence of p-toluenesulfonic acid gave the 2′, 3′-isopropylidene derivative (6a). Phosphorylation of 6a with phosphoryl chloride and triethylphosphate followed by treatment with barium hydroxide afforded barium 3,4-diphenyl-4,5-dihydro(β-D-ribofuranosyl)-1,2,4-triazole-5-thione-5′- monophosphate, which gave after lyophilization the free acid (7a)     

9-(2-Deoxy-ß-D-xylofuranosyl)adenine and 1-(2-Deoxy-ß-D-xylofuranosyl)thymine: Phosphorylation and Stability

Abstract

Phosphorylation of 1-(2-deoxy-β-D-xylofuranosyl)thymine (1) or 9-(2-deoxy-β-D-xylofuranosyl)adenine (3) with phosphoryl chloride gives the cyclic 3′,5′-phosphates (2 and 4a) but not the 5′-monophosphates 8a or 8b. The latter are obtained by phosphorylation of the 3′-0-benzoylated 2′-deoxy-β-D-xylonucleosides (7a, b) and subsequent base-catalyzed removal of the benzoyl groups. Compound 3, as the parent dA, depurinates in acidic medium, a reaction which is facilitated in the case of the N⁶-benzoyl derivative 9b and reduced after the introduction of an amidine protecting group. N-Glycosylic bond hydrolysis of 2′-deoxy-β-D-xylofuranosyl nucleosides is enhanced by a factor of two compared to 2′-deoxy-β-D-ribofuranosyl nucleosides.     

C-Nucleosides via Glycosyl Alkynyl Ketones. Synthesis of 5(3)-Phenyl-3(5)-(β-D-ribofuranosyl) Pyrazole

Abstract

A β-D-ribofuranosyl phenylethynyl ketone (3) has been synthesized and shown to be a suitable intermediate for heterocyclic elaboration to C-nucleosides. Cyclization of 3 with hydrazine hydrate produces the title C-nucleoside.     

Nucleosides. LXII. Synthesis of 6-Methyl-8-(2-deoxy-β-D-ribofuranosyl)-isoxanthopterin and Derivatives

Abstract

The syntheses of 6-methyl-8-(2-deoxy-ß-D-ribofuranosyl)isoxanthopterin (21) and its protected 3′-O-phosphoramidite 23 were achieved from 6-methyl-2-methylthio-8-(2-deoxy-3,5-di-O-p-toluoyl-ß-D-ribofuranosyl)-3H,8H-pteridine-4,7-dione (8) in several steps. The new building block for oligonucleotide syntheses is highly fluorescent and can be considered as a substitute for 2′-deoxyguanosine.     

4-Substituted-5(3)-carbamoyl-3(5)-(2-deoxy-β-D-ribofuranosyl)pyrazoles. Application of Palladium Catalyzed Glycal Coupling Methodology to the Synthesis of Pyrazofurin Analogs

Abstract

Analogs of the C-nucleoside pyrazofurin were prepared in 7–9 steps using a key Pd(0)- catalyzed coupling reaction between protected iodopyrazoles 6a and 6b and glycal 8 to form the glycosyl bond. Conditions for this reaction were improved from those previously described for related reactions in order to maximize product yields and eliminate the need for triphenylarsine.

     

Oligonucleotide–Minor Groove Binder Conjugates and Their Complexes with Complementary DNA: Effect of Conjugate Structural Factors on the Thermal Stability of Duplexes

Synthetic polycarboxamide minor groove binders (MGB) consisting of N‐methylpyrrole (Py), N‐methylimidazole (Im), N‐methyl‐3‐hydroxypyrrole (Hp) and β‐alanine (β) show strong and sequence‐specific interaction with the DNA minor groove in side‐by‐side antiparallel or parallel orientation. Two MGB moieties covalently linked to the same terminal phosphate of one DNA strand stabilize DNA duplexes formed by this strand with a complementary one in a sequence‐specific manner, similarly to the corresponding mono‐conjugated hairpin structures. The series of conjugates with the general formula Oligo‐(L‐MGB‐R)_m was synthesized, where m = 1 or 2, L = linker, R = terminal charged or neutral group, MGB = –(Py)_n–, –(Im)_n– or –[(Py/Im)_n–(CH₂)₃CONH–(Py/Im)_n–] and 1 < n < 5. Using thermal denaturation, we studied effects of structural factors such as m and n, linker L length, nature and orientation of the MGB monomers, the group R and the backbone (DNA or RNA), etc. on the stability of the duplexes. Structural factors are more important for linear and hairpin monophosphoroamidates than for parallel bis‐phosphoroamidates. No more than two oligocarboxamide strands can be inserted into the duplex minor groove. Attachment of the second sequence‐specific parallel ligand [–L(Py)₄R] to monophosphoroamidate conjugate CGTTTATT–L(Py)₄R leads to the increase of the duplex Tm, whereas attachment of [–L(Im)₄R] leads to its decrease. The mode of interaction between oligonucleotide duplex and attached ligands could be different (stacking with the terminal A:T pair of the duplex or its insertion into the minor groove) depending on the length and structure of the MGB.     

Definitive Solution Structures for the 6-Formylated Versions of 1-(βD-Ribofuranosyl)-, 1-(2′-Deoxy-β-D-Ribofuranosyl)-, and 1-β-D-Arabinofuranosyluracil,and of Thymidine

Abstract

ROESY and NOESY NMR spectroscopic analyses of the ribofuranosyl (1a), 2′-deoxyribofuranosyl (1b), and arabinofuranosyl (1c) derivatives of 6-formyluracil in (CD₃)₂SO and D₂O solutions have established that each exclusive 7,05′-cyclic hemiacetal diastereomer of 1a,b and the major 7,O2′-cyclic hemiacetal diastereomer of 1c possess the 7R configuration. In addition, (7R)-1c has been shown to be thermodynamically more stable than (7S)-1c, contrary to our previous indication. A new, higher yielding synthetic route to 1a has been developed, 1b has been obtained for the first time in crystalline form, the route to 1c has been modified to better accommodate large scale preparations, and a new, fourth member of this class, 6-formylthymidine (1d), has been synthesized and its solution structures in (CD₃)₂SO, D₂O, and CD₃OD have been determined. Antitumor and antiviral evaluations of 1a-c have revealed no significant levels of activity.     

Synthesis and Antiviral Activities of 5-Substituted 1-(2-Deoxy-2-C-methylene-4-thio-β-D-erythro-pentofuranosyl)uracilst†

Abstract

Various 5-substituted 1-(2-deoxy-2-C-methylene-4-thio-β-D-erythropentofuranosyl)uracils (4′-thioDMDUs) were synthesized from D-glucose via sila-Pummerer-type glycosylation. All of the β-anomers of 5-substituted 4′-thioDMDU, except the 5-hydroxyethyl derivative, showed potent anti-HSV-1 activity (ED₅₀ = 0.016–0.096 μg/mL). 5-Ethyl- and 5-iodo-4′-thioDMDUs were also active against HSV-2 (ED₅₀ = 0.17 and 0.86 μg/mL, respectively). 5-Bromovinyl-4′-thioDMDU was particularly active against VZV (ED₅₀ = 0.013 μg/mL).

     

Synthesis and AcidBase Properties of an Imidazole-Containing Nucleotide Analog, 1-(2'-Deoxy-β-D-ribofuranosyl)imidazole 5'-Monophosphate (dImMP(2-) )

Deletion of the substituted pyrimidine ring in purine-2'-deoxynucleoside 5'-monophosphates leads to the artificial nucleotide analog dImMP(2-) . This analog can be incorporated into DNA to yield, upon addition of Ag(+) ions, a molecular wire. Here, we measured the acidity constants of H(2) (dImMP)(±) having one proton at N(3) and one at the PO$\rm{{_{3}^{2-}}}$ group by potentiometric pH titrations in aqueous solution. The micro acidity constants show that N(3) is somewhat more basic than PO$\rm{{_{3}^{2-}}}$ and, consequently, the (H??dImMP)(-) tautomer with the proton at N(3) dominates to ca. 75%. The calculated micro acidity constants are confirmed by (31) P- and (1) H-NMR chemical shifts. The assembled data allow many quantitative comparisons, e.g., the N(3)-protonated and thus positively charged imidazole residue facilitates deprotonation of the P(O)(2) (OH)(-) group by 0.3?pK units. Information on the intrinsic site basicities also allows predictions about metal-ion binding; e.g., Mg(2+) and Mn(2+) will primarily coordinate to the phosphate group, whereas Ni(2+) and Cu(2+) will preferably bind to N(3). Macrochelate formation for these metal ions is also predicted. The micro acidity constant for N(3)H(+) deprotonation in the (H???dImMP?H)(±) species (pk(a) 6.46) and the M(n+) -binding properties are of relevance for understanding the behavior of dImMP units present in DNA hairpins and metalated duplexes.     

The Stability of Trisubstituted Internucleotide Bond in the Presence of the Vicinal 2′-Hydroxyl. Chemical Synthesis of Uridyl(2′-phosphate)-(3′-5′)-uridine

Abstract

The effect of eleven different phosphoryl center protecting groups on the stability of trisubstituted internucleotide bond of the dimers (1a-k), in the presence of the vicinal 2′-hydroxyl, was examined. It has been found that electronic properties of the phosphoryl center protecting groups are essential for the reactivity of the trisubstituted internucleotide bond. Those observations were applied to the chemical synthesis of the uridyl(2′-phosphate)-(3′-5′)-uridine, a useful model for further pre-tRNA splicing studies.     

A Convenient Synthesis of A Novel Nucleoside Analogue: 4-(δ-Diformyl-methyl)-1-(β-D-ribofuranosyl)-2-pyrimidinone

Abstract

The nucleoside analogue 4-(δ-diformyl-methyl)-1-(β-D-ribofuranosyl)-2-pyrimidinone (5) was prepared from the corresponding 4-methyl pyrimidinone nucleoside by means of the Vilsmeier reaction. The unprotected nucleoside can be phosphorylated directly with phosphorus oxychloride in triethyl phosphate.     

Evaluation of the Kinetics of Hydrolysis of Monoamino Analogues of 2′- or 3′-Deoxyadenosine and of 9-(2-Deoxy-β-D-Threo-pentofuranosyl)Adenine or 9-(3-Deoxy-β-D-threo-pentofuranosyl)Adenine by Liquid Chromatography

Abstract

Liquid chromatography was used to follow the degradation of monoamino analogues of 2′- or 3′-deoxyadenosine and of 9-(2-deoxy-β-D-threo-pentofuranosyl) adenine or 9-(3-deoxy-β-D-threo-pentofuranosyl) adenine in buffers of different pH and constant ionic strength (μ). Comparison of stabilities of some of the compounds under study with those of corresponding hydroxyl analogues showed that at acid pH the aminated compounds are more stable than the corresponding hydroxyl compounds. The higher stability associated with the presence of an amino group in the sugar is explained in function of pK_a values, which were determined by ¹³C NMR.